Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study
Abstract
Lateral gene transfer (LGT) is now accepted as an important factor in the evolution of prokaryotes. Establishment of the occurrence of LGT is typically attempted by a variety of methods that includes the comparison of reconstructed phylogenetic trees, the search for unusual GC composition or codon usage within a genome, and identification of similarities between distant species as determined by best BLAST hits. We explore quantitative assessments of these strategies to study the prokaryotic trait of nitrogen fixation, the enzyme-catalyzed reduction of N2 to ammonia. Phylogenies constructed on nitrogen fixation genes are not in agreement with the tree-of-life based on 16S rRNA but do not conclusively distinguish between gene loss and LGT hypotheses. Using a series of analyses on a set of complete genomes, our results distinguish two structurally distinct classes of MoFe nitrogenases whose distribution cuts across lines of vertical inheritance and makes us believe that a conclusive case for LGT has been made.
- Publication:
-
Proceedings of the National Academy of Science
- Pub Date:
- June 2006
- DOI:
- 10.1073/pnas.0603534103
- Bibcode:
- 2006PNAS..103.9584K
- Keywords:
-
- PHYSICAL SCIENCES / BIOLOGICAL SCIENCES / STATISTICS / EVOLUTION